removeLocalTagAnomalies: Removes loval anomalies

In ChIC: Quality Control Pipeline for ChIP-Seq Data

Description

The removeLocalTagAnomalies function removes tags from regions with extremely high tag counts compared to the neighbourhood.

removeLocalTagAnomalies

Usage

removeLocalTagAnomalies(chip, input, chip_b.characteristics,
    input_b.characteristics)

Arguments

chip,	data-structure with tag information for the ChIP (see readBamFile())
input,	data-structure with tag information for the Input (see readBamFile())
chip_b.characteristics	binding.characteristics of the ChIP. Is a data-structure containing binding information for binding peak separation distance and cross-correlation profile (see get.binding.characteristics)
input_b.characteristics,	binding.characteristics of the Input. Is a data-structure containing binding information for binding preak separation distance and cross-correlation profile (see get.binding.characteristics)

Value

result A list containing filtered data structure for ChIP and Input

Examples

## This command is time intensive to run
##
## To run the example code the user must provide two bam files for the ChIP
## and the input and read them with the readBamFile() function. To make it
## easier for the user to run the example code we provide tow bam examples 
## (chip and input) in our ChIC.data package that have already been loaded 
##with the readBamFile() function.

mc=4
## Not run: 

filepath=tempdir()
setwd(filepath)

##load the data
data("chipSubset", package = "ChIC.data", envir = environment())
chipBam=chipSubset
data("inputSubset", package = "ChIC.data", envir = environment())
inputBam=inputSubset

## calculate binding characteristics 

chip_binding.characteristics<-spp::get.binding.characteristics(
chipBam, srange=c(0,500), bin=5,accept.all.tags=TRUE)

input_binding.characteristics<-spp::get.binding.characteristics(
inputBam, srange=c(0,500), bin=5,accept.all.tags=TRUE)

##get chromosome information and order chip and input by it
chrl_final=intersect(names(chipBam$tags),names(inputBam$tags))
chipBam$tags=chipBam$tags[chrl_final]
chipBam$quality=chipBam$quality[chrl_final]
inputBam$tags=inputBam$tags[chrl_final]
inputBam$quality=inputBam$quality[chrl_final]

##remove sigular positions with extremely high read counts with 
##respect to the neighbourhood
selectedTags=removeLocalTagAnomalies(chipBam, inputBam, 
chip_binding.characteristics, input_binding.characteristics)

## End(Not run)

ChIC documentation built on Nov. 8, 2020, 5:15 p.m.